FILTLONG

Quality filtering tool for long reads.

Example

This wrapper can be used in the following way:

rule filtlong:
    input:
        reads = "{sample}.fastq"
    output:
        "{sample}.filtered.fastq"
    params:
        extra=" --mean_q_weight 5.0",
        target_bases = 10
    log:
        "logs/filtlong/test/{sample}.log"
    wrapper:
        "0.75.0-7-g74e079c/bio/filtlong"

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

  • filtlong=0.2.0=he941832_2

Authors

  • Michael Hall

Code

"""Snakemake wrapper for filtlong."""

__author__ = "Michael Hall"
__copyright__ = "Copyright 2019, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"


from snakemake.shell import shell

# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")
target_bases = int(snakemake.params.get("target_bases", 0))
if target_bases > 0:
    extra += " --target_bases {}".format(target_bases)

# Formats the log redrection string
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Executed shell command
shell("filtlong {extra}" " {snakemake.input.reads} > {snakemake.output} {log}")